Hello Hiren, (reply below) On Tue, 2013-07-09 at 16:59 +0200, Hiren Ghosh wrote: > Dear All, I used MIRA for genome assembly and i got contigfile " > Ecoli-1_out.unpadded.fasta". Now i want to do alignment with this > contig with another Ecoli genome " refseq.fasta". In command line i am > typinglike this and getting error message. > Attempt 1: ./mauveAligner --output=ec_ec.mauve > --output-alignment=ec_vs_ec.alignment Ecoli-1_out.unpadded.fasta > refseq.fasta Sequence loaded successfully. Ecoli-1_out.unpadded.fasta > 4982364 base pairs. Using weight 15 mers for initial seeds Creating > sorted mer list Create time was: 2 seconds. > 0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..10%.. > 11%..12%..13%..14%..15%..16%..17%..18%..19%..20%.. > 21%..22%..23%..24%..25%..26%..27%..28%..29%..30%.. > 31%..32%..33%..34%..35%..36%..37%..38%..39%..40%.. > 41%..42%..43%..44%..45%..46%..47%..48%..49%..50%.. > 51%..52%..53%..54%..55%..56%..57%..58%..59%..60%.. > 61%..62%..63%..64%..65%..66%..67%..68%..69%..70%.. > 71%..72%..73%..74%..75%..76%..77%..78%..79%..80%.. > 81%..82%..83%..84%..85%..86%..87%..88%..89%..90%.. > 91%..92%..93%..94%..95%..96%..97%..98%..99%..Starting with 0 MUMs > Eliminating overlaps yields 0 MUMs
In this case, mauveAligner was unable to find any exact matches of length 15 or greater among your input sequences. This generally happens when the genomes are too divergent to be aligned at the nucleotide level. Unless you want mauveAligner for some historical reason, I suggest you use progressiveMauve if possible since it can align more divergent genomes than mauveAligner and is generally more accurate. However, if mauveAligner couldn't find any matches at all, progressiveMauve will probably not do much better. Check that your refseq input file does in fact contain sequence data -- there was only one message in the output above giving the sequence size but that is usually printed for both sequences. > Attempt2: ./mauveAligner --output=jb50vsSpmito.mauve > --output-alignment=jb50vsSpmito.alignment Ecoli-1_out.unpadded.fasta > jb50contigs.fa.sslist refseq.fasta Sp.may2011.extras_mito.fasta.sslist > Sequence loaded successfully. Ecoli-1_out.unpadded.fasta 4982364 base > pairs. Sequence loaded successfully. refseq.fasta 2435000 base pairs. > Using weight 15 mers for initial seeds Creating sorted mer list Create > time was: 2 seconds. Creating sorted mer list ERROR! gap character > encountered at genome sequence position 61 Input sequences must be > unaligned and ungapped! Unlike many errors generated by Mauve, this error message is pretty self-explanatory. There is some kind of non-nucleotide character in your input sequence. I think MIRA assembler output includes non-nucleotide characters in some cases. Check the MIRA documentation and fix your input files accordingly. Best, -Aaron -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. ------------------------------------------------------------------------------ See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
